It definitely would!

Dean would still be jumpy if he ran into Sam without warning, but he’s also not about to bother a person just minding their own business getting supplies. He’d be more likely to let them go and see if they knew anything about the problems Trails West has been having, since borrowers/littles are a very good source of information for the hunters that protect them.

So they would definitely still meet, Dean would grab Sam, let him go, probably with a warning that something’s up in the motel, and Sam wouldn’t be able to resist giving Dean a hand with it, only to discover just who Dean is in the first place.